Errata

Genbank
->
GenBank

## This is confirmed.

########################################

Genbank
->
GenBank

## This is confirmed.

########################################

itself or an adjunct to ongoing investigations.
->
itself, or as an adjunct to ongoing investigations.

########################################

and the computer program.
->
and computer programming.

########################################

a link to the brain tumors you suspect exist.
->
a role in tumor development.

########################################

metaphor between the two disciplines.)
->
metaphor.)

########################################

large, programmable, digital/electronic (the ENIAC) computers.
->
large-scale, programmable, digital, electronic computers (such as ENIAC).

########################################

it's done so left to right
->
it's usually written left to right

########################################

It can appear as
->
It can appear in

########################################

most of the life
->
much of the life

########################################

easy to identify
->
easy to calculate the

########################################

such as the intriguing processes of
->
for instance, the intriguing techniques of

########################################

related by virtue of their protein products as part of
->
related by virtue of their protein products being part of

########################################

Mac, then
->
Mac, and then

########################################

several books such as O'Reilly's Perl Resource Kits,
->
several books

## The reader comments:
## I would suggest to remove "such as O'Reilly's Perl Resource Kits,".
## There is only the Win32 version still available, and even this version
## is totally outdated and much too expensive for the audience of this book.

## Tisdall says: sounds plausible to me: editors, how say you??

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

beginners, there's
->
beginners: there's

########################################

remember that
->
remember

########################################

perl example4 -1
->
perl example4-1

## This is confirmed.

########################################

more easily read
->
more easily readable

########################################

and to make sure
->
and its output to make sure that

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

to the right
->
on the right

########################################

new and successful way.
->
new and successful approach.

########################################

You can use any name
->
You can use any name for the file

########################################

both are listed in
->
both are demonstrated in

########################################

is assigned each time through the loop to
the next line of the file
->
is assigned to the next line of the file
each time through the loop

########################################

the type of input it gets.
->
the type of input the program gets.

########################################

Example 5-3, in Chapter 9, and
->
Example 5-3; in Chapter 9; and

########################################

characters, which is done globally
->
characters. This deletion is done globally

########################################

line, and a formfeed advances to the next line. The two of them
together amount to the same thing as a newline character.
->
line. Perl newlines are handled differently on different operating systems;
briefly,
works on all, but you may see
at the end of lines on Windows.

## This is confirmed.

########################################

We now have a design for the program, let's
->
Now that we have a design for the program, let's

########################################

is the same as previous
->
is the same as in previous

########################################

decimal or floating-point numbers
->
decimal (or floating-point) numbers
## italicise "floating-point"

########################################

or Perl documentation
->
or the Perl documentation

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

regularly
->
often

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

reading from, and writing to, files as well as other actions.
->
reading from files and writing to files, as well as other actions.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

while($dna =~ /a/ig){$a++}
Should be:
while($DNA =~ /a/ig){$a++}

4th line from top;
$dna =~ /a/ig
should be:
$DNA =~ /a/ig

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

also has the global modifier,
->
also has the global modifier g,

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

you'll use those while loops to good effect
->
you'll use while loops in a similar fashion, to good effect

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

The program, however,
->
The program, moreover,

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

($dna = ~ tr/ACGTacgt//)
->
($dna =~ tr/ACGTacgt//)
There shouldn't be a space between = and ~

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

(eq actually an operator).
->
(eq is actually an operator).

## This is confirmed.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

(Hint: you can use the Perl functions substr or slice.
->
(Hint: you can use the Perl functions substr or splice.)

## This is confirmed

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

mean of a distribution at
->
mean of a distribution, at

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

so-called recursion
->
## italicise "recursion"

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

The trick of all
->
The trick to all

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

We'll now look at this code
->
We'll now look more closely at this code

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

seen earlier in loops and conditional statements that groups
->
as the block used in a loop to group

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

You use the command line
->
You'll also use the command line

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

# Chapter Four, "Motifs and Loops"
->
# Chapter Five, "Motifs and Loops"

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

In the example of pass-by-reference in this section
->
In the example of pass-by-reference later in this section

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

passed on as arguments.
->
passed in as arguments.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

appear in multiple program.
->
appear in multiple programs.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

Beginning in Chapter 8, I'll define subroutines and show the code, but you'll be
putting them into your module and typing:
->
All the useful subroutines in this book will be put into this module, which
you'll start using in Chapter 8 by typing:

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

step you through that code as well.
->
steps you through that code as well.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

The paragraph before the code:
"If you wish to see more lines, the w or "window" command will serve"
w adds a watch. It Should be v
"If you wish to see more lines, the v or "window" command will serve"

#######################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

Books states:

DB<12> D
Deleting all breakpoints..

But it should be:
DB<21> B *
Deleting all breakpoints...

#######################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

DB<13> w 45

Should it be
DB<13> v 45

######################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

Book states
DB<12> W $receivingcommittment

But should be w (lowercase)
DB<12> w $receivingcommittment

#######################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

Book
You see that at line 66 you misspelled

Should be
You see that at line 46 you misspelled

#######################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

Book states
"So fix the misspelling at line 66"

Should be
"So fix the misspelling at line 46"

#######################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

nonviable offspring that dies
->
nonviable offspring that die

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

they can lead to evolutionary
->
mutations can lead to evolutionary

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

the first and last sentences of this paragraph are redundant and one could be cut (I
would recommend cutting the last sentence).

first sentenct: "In the examples that follow, I use a simple Perl Method for seed
picking that's okay for most purposes."

last sentence: "In this book, I use a Perl method that is good enough for most
purposes."

######################################

Note from the Author or Editor:
Error corrected. Will be fixed for next printing.

that do the test first and then the block.
->
that test first and then do the block.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

is really a short function
->
is a very short subroutine

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

It's just like the idea in
->
It's a subroutine to select a string position, very similar to the idea in

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

picking a random position then
->
picking a random position, then

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

have to do that a lot
->
have to look things up a lot

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

main program and proceeds, following the order of the
top-down design you did in pseudocode,
then followed by the subroutines.
->
main program and is followed by the subroutines,
in the same order as the top-down design you did in pseudocode.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

nucleotide in the same position
->
nucleotides in the same positions

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

(indexed by $K)

should be
(indexed by $k)

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

Sometimes not all choices are will be picked
->
Sometimes not all choices are equally likely to be picked

## This is confirmed.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

couldn't respond
->
couldn't respond informatively

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

You might try storing
->
You could store

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

in an array, for example, to search
->
in an array. For example, to search

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

databases. Some good ones that are free
->
databases, some good ones that are free

## This is confirmed.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

Herein
->
Here

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

code, and the last subroutine clearly displays this redundancy.
It might be interesting to express that in your subroutine.
->
code, and subroutine codon2aa clearly maps several codons to the
same amino acid. We can represent this redundancy another way.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

let's try to redo the subroutine
->
let's rewrite subroutine codon2aa

######################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

$codon
->
## could be formatted in nonproportional font

## Tisdall says: editors, how say you???

#######################################

condon2aa
->
codon2aa

## This is confirmed.

###########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

"$codon = substr ($dna, $i 3);" should be
"$codon = substr ($dna, $i, 3);"

## This is confirmed.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

biologists and programmers invented
->
biologists and programmers have invented

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

would think incorrectly, that the file
->
would think, incorrectly, that the file

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

As you accumulate useful subroutines in our modules,
->
As you accumulate useful subroutines in modules,

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

where in the DNA you're studying the cell
->
where, in the DNA you're studying, the cell

#########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

## The equation should be reformatted so that:

+1
->
+ 1

#######################################

Pseudocode line near the bottom of the page, above last paragraph;
This is pseudocode, so it doesn't have to be perfect, but as written this line
looks like some kind of strange assignment instead of a comparison:

"(end - 1) - (start - 1) + 1 = end - start +1"

I'm not sure what the best way to fix this is. It is set in the monospace font
used for pseudocode & real code, but it isn't quite either, so I was going to s
uggest re-setting it in the variable width font used in the main text. That pro
bably won't clarify it either though, so the equals sign should probably just b
e doubled so that it's clear that the line is a comparison, and not an assignme
nt.

## Tisdall replies:
## This report is (kind of) confirmed. The line in question is an
## equation from elementary algebra.
## = as assignment in programming languages, and = as equality
## in algebra and much other mathematics, is indeed confusing
## (and has already been discussed), therefore let me add:

So let's write this subroutine:
->
as we know from algebra. So let's write this subroutine:

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

an.d
->
and

## This report is confirmed.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

documentation (or Appendix B), for
->
documentation (or Appendix B) for

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

for each enzyme.To simplify matters
->
for each enzyme. To simplify matters

#######################################

Note from the Author or Editor:
Error corrected. Will fixed in next printing.

the documentation on REBASE you found on its web site
->
the documentation from the REBASE web site

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

It's bad, because that same flexibility makes it harder to write programs that to
find and extract the desired annotations.
->
It's bad, because that same flexibility makes it harder to write programs that
find and extract the desired annotations.

## This is confirmed.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

contains 12,813516 loci and
->
contains

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

(typical)) foreach{ ... } section of the parse1() subroutine, starting at
middle of page;
Most of the book's code is pretty clear & consistent, but one thing that the au
thor keeps wavering on is the inclusion or omission of spaces on lines like the
ones here. Appreviating, the code here has these lines:

} elseif( $in_sequence) {
} elseif ( $line =~ /^ORIGIN/ ) {
} else{

Note that the second elsif is followed by a space, but the first one isn't and
neither is the else. Likewise, $in_sequence has a leading space but not a trail
ing one.

## This report is correct. In this code fragment it does interfere with readability.
## Since the code is so dense here, I'd prefer:
if ( $line =~ /^//
/ ) {
}elseif ( $in_sequence ) {
}elseif ( $line =~ /^ORIGIN/ ) {
}else {
## But in general it's a deliberate choice to vary these things. 1) All such variations
## are legal Perl, and for good reason. 2) Beginners are likely to encounter such
## variations as they encounter different programming styles. 3) Beginners experiment
## with different styles as they develop their own preferences, so 4) I show the
## beginners different styles, and discuss the issue in the book.
##
## I am fully aware of the reason for standards for such formatting issues.
## However, I feel even in professional code they are not an unbreakable rule,
## and that readability is paramount. (You may feel that the only way to
## ensure readability is to follow a rule consistently, but I disagree.)

########################################

like so: m!//
!).
->
like so: m!^//
! where the expression is now ^//
).

#########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

so it extends the ^ and the $
to match after, or before, a newline, embedded in the string.
->
so it extends the ^ to match after an embedded newline,
and the $ to match before an embedded newline.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

First, let's examine
->
Let's examine

########################################

Note from the Author or Editor:
Error corrected. Will be fixed for the next printing.

"I then saved the output as text in the file blst.txt, which is available from this..."
blst.txt
should be
blast.txt

########################################

the effect on biology and medicine would be profound.
->
the effect on biology and medicine will be profound.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

you can give the directory name the special name "." for the current directory,
->
you can just call the directory by the special name ".",

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

given an scalar containing SEQRES lines,
->
given a scalar containing SEQRES lines,

## This is confirmed.

#######################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

In Chapter 10, I demonstrated two ways to parse GenBank files into sequence and
annotation and then how to parse the annotation into finer and finer levels of detail.
->
In Chapter 10, I compared two ways to parse GenBank files into sequence and
annotation, and to parse the annotation into finer and finer levels of detail.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

what field the input line was in.
->
which section of the file each input line came from.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

captures the pattern matched, denoted by $&
->
copies the pattern matched, denoted by the special variable $& that always holds
the last successful pattern match,

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

Let's examine the subroutine extractSEQRES, now that the record types have been
parsed out, and extract the primary amino acid sequence.
->
Now that the record types have been parsed out, let's examine the subroutine extractSEQRES,
and see how it extracts the primary amino acid sequence.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

Our success with the previous parsePDBrecordtypes subroutine that used iteration
over lines (as opposed to regular expressions over multiline strings)
leads to the same approach here.
->
Our success in parsePDBrecordtypes using iteration over lines
(as opposed to regular expressions over multiline strings)
leads us to try the same approach here.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

get_two__atoms
->
get_two_atoms

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

The actual running of the program and collecting its output happens in just one line.
->
The actual running of the program and collecting its output happen in just one line.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

There are a several
->
There are several

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

before and after embedded newlines.
->
before and after embedded newlines, respectively.

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

FORTRAN programming-language conventions
->
FORTRAN programming language conventions

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

I've frequently mentioned modules and CPAN
->
I've frequently mentioned modules, and CPAN

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

the thousand of genes and gene products
->
the genes and gene products

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.

Graphics programming language present
->
Graphics programming languages present

########################################

Note from the Author or Editor:
Error corrected. Will be fixed in next printing.